rs61750878
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001012659.2(ARGFX):c.587C>T(p.Thr196Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.005 in 1,614,032 control chromosomes in the GnomAD database, including 359 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001012659.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ARGFX | NM_001012659.2 | c.587C>T | p.Thr196Ile | missense_variant | 5/5 | ENST00000334384.5 | NP_001012677.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ARGFX | ENST00000334384.5 | c.587C>T | p.Thr196Ile | missense_variant | 5/5 | 3 | NM_001012659.2 | ENSP00000335578.3 | ||
ARGFX | ENST00000651603.1 | c.587C>T | p.Thr196Ile | missense_variant | 4/4 | ENSP00000498601.1 |
Frequencies
GnomAD3 genomes AF: 0.0266 AC: 4051AN: 152152Hom.: 182 Cov.: 32
GnomAD3 exomes AF: 0.00701 AC: 1760AN: 251170Hom.: 78 AF XY: 0.00530 AC XY: 720AN XY: 135740
GnomAD4 exome AF: 0.00274 AC: 4006AN: 1461762Hom.: 177 Cov.: 32 AF XY: 0.00239 AC XY: 1738AN XY: 727184
GnomAD4 genome AF: 0.0267 AC: 4060AN: 152270Hom.: 182 Cov.: 32 AF XY: 0.0255 AC XY: 1899AN XY: 74454
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at